[ARVADOS] created: 1.1.2-38-g9bb7230

[Git user]

        at  9bb723068bdba79d9bc6272697c353cac5fda40d (commit)


commit 9bb723068bdba79d9bc6272697c353cac5fda40d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue Jan 9 10:20:14 2018 -0500

    12921: Fix outputTTL to apply to RunInSingleContainer
    
    Arvados extensions should not propagate to workflow inside the
    container (which is run using cwltool), but do need to propagate to
    RunInSingleContainer CommandLineTool.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index d426c1a..79bfacd 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -158,7 +158,7 @@ class ArvadosWorkflow(Workflow):
                 "inputs": self.tool["inputs"],
                 "outputs": self.tool["outputs"],
                 "stdout": "cwl.output.json",
-                "requirements": workflowobj["requirements"]+[
+                "requirements": self.requirements+[
                     {
                     "class": "InitialWorkDirRequirement",
                     "listing": [{
@@ -172,7 +172,7 @@ class ArvadosWorkflow(Workflow):
                             "entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }]
                 }],
-                "hints": workflowobj["hints"],
+                "hints": self.hints,
                 "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
             })
             kwargs["loader"] = self.doc_loader
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index cfb2fa4..d99cf6c 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -128,3 +128,9 @@
   output: {}
   tool: secondary/wf.cwl
   doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml"
+
+- job: null
+  output:
+    out: out
+  tool: wf/runin-with-ttl-wf.cwl
+  doc: "RunInSingleContainer respects outputTTL"
diff --git a/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
new file mode 100644
index 0000000..713e0c0
--- /dev/null
+++ b/sdk/cwl/tests/wf/runin-with-ttl-wf.cwl
@@ -0,0 +1,63 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+class: Workflow
+cwlVersion: v1.0
+$namespaces:
+  arv: "http://arvados.org/cwl#"
+inputs:
+  fileblub:
+    type: File
+    default:
+      class: File
+      location: keep:d7514270f356df848477718d58308cc4+94/a
+      secondaryFiles:
+        - class: File
+          location: keep:d7514270f356df848477718d58308cc4+94/b
+outputs:
+  out:
+    type: string
+    outputSource: substep/out
+requirements:
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+hints:
+  arv:IntermediateOutput:
+    outputTTL: 60
+steps:
+  substep:
+    in:
+      fileblub: fileblub
+    out: [out]
+    hints:
+      - class: arv:RunInSingleContainer
+    run:
+      class: Workflow
+      id: mysub
+      inputs:
+        fileblub: File
+      outputs:
+        out:
+          type: string
+          outputSource: cat1/out
+      steps:
+        cat1:
+          in:
+            fileblub: fileblub
+          out: [out]
+          run:
+            class: CommandLineTool
+            id: subtool
+            inputs:
+              fileblub:
+                type: File
+                inputBinding: {position: 1}
+            outputs:
+              out:
+                type: string
+                outputBinding:
+                  outputEval: "out"
+            baseCommand: cat

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